Field of the Invention
The present invention relates to a computer assisted system and method for determining and displaying chemical structures useful in the design of single chain proteins.
Description of the Background Art
The advent of modern molecular biology and immunology has brought about the possibility of producing large quantities of biologically active materials in highly reproduceable form and with low cost. Briefly, the gene sequence coding for a desired natural protein is isolated, replicated (cloned) and introduced into a foreign host such as a bacterium, a yeast (or other fungi) or a mammalian cell line in culture, with appropriate regulatory control signals. When the signals are activated, the gene is transcribed and translated, and expresses the desired protein. In this manner, such useful biologically active materials as hormones, enzymes or antibodies have been cloned and expressed in foreign hosts.
One of the problems with this approach is that it is limited by the "one gene, one polypeptide chain" principle of molecular biology. In other words, a genetic sequence codes for a single polypeptide chain. Many biologically active polypeptides, however, are aggregates of two or more chains. For example, antibodies are three-dimensional aggregates of two heavy and two light chains. In the same manner, large enzymes such as aspartate transcarbamylase, for example, are aggregates of six catalytic and six regulatory chains, these chains being different. In order to produce such complex materials by recombinant DNA technology in foreign hosts, it becomes necessary to clone and express a gene coding for each one of the different kinds of polypeptide chains. These genes can be expressed in separate hosts. The resulting polypeptide chains from each host would then have to be reaggregated and allowed to refold together in solution. Alternatively, the two or more genes coding for the two or more polypeptide chains of the aggregate could be expressed in the same host simultaneously, so that refolding and reassociation into the native structure with biological activity will occur after expression. The approach, however, necessitates expression of multiple genes, and as indicated, in some cases, in multiple and different hosts. These approaches have proved to be inefficient.
Even if the two or more genes are expressed in the same organism it is quite difficult to get them all expressed in the required amounts.
A classical example of multigene expression to form multimeric polypeptides is the expression by recombinant DNA technology of antibodies. Genes for heavy and light chains have been introduced into appropriate hosts and expressed, followed by reaggregation of these individual chains into functional antibody molecules (see for example Munro, Nature, 312:597 (1984); Morrison, S. L. Science 229:1202 (1985); Oi et al., BioTechniques 4:214 (1986).
Antibody molecules have two generally recognized regions in each of the heavy and light chains. These regions are the so-called "variable" region which is responsible for binding to the specific antigen in question, and the so-called "constant" region which is responsible for biological effector responses such as complement binding, etc. The constant regions are not necessary for antigen binding. The constant regions have been separated from the antibody molecule, and biologically active (i.e. binding) variable regions have been obtained.
The variable regions of an antibody are composed of a light chain and a heavy chain. Light and heavy chain variable regions have been cloned and expressed in foreign hosts, and maintain their binding ability (Moore et al, European Patent Publication No. 0088994 (published Sept. 21, 1983)).
It would be much more efficient if one could produce single polypeptide-chain molecules which have the same biological activity as the multiple chain aggregates such as, for example, multiple chain antibody aggregates or enzyme aggregates. Given the "one gene-one-polypeptide chain" principle, such single chain molecules would be more readily produceable, and would not necessitate multiple hosts or multiple genes in the cloning and expression. In order to accomplish this, it is first necessary to devise a method for generating single chain structures from two-chain aggregate structures, wherein the single chain will retain the three-dimensional folding of the separate natural aggregate of two polypeptide chains.
While the art has discussed the study of proteins in three dimensions, and has suggested modifying their architecture (see, for example, the article "Protein Architecture: Designing from the Ground Up," by Van Brunt, J., BioTechnology, 4: 277-283 (April 1986)), the problem of generating single chain structures from multiple chain structures, wherein the single chain structure will retain the three-dimensonal architecture of the multiple chain aggregate, has not been satisfactorily addressed.